Local campaing’s results (PhD Chapter 1)

This series of files compile all analyses done during Chapter 1 for the local campaign (2014):

All analyses have been done with PRIMER-e 6 and R 3.6.0.

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Caracteristics of each campaign

2014 2016 2017
Sampling date August-September June to August July
Criteria for perturbation Potentially impacted if close to the city or industries, References outside the bay Human-impacted if in a region with a highly populated area, industries and maritime activities, Reference if none of these criteria Human-impacted if in a region with a highly populated area, industries and maritime activities, Reference if none of these criteria
Regions considered BSI BSI, CPC, BDA, MR BSI, MR
Number of sampled stations 40 (20 HI, 20 R) 78 (26 BSI, 19 CPC, 18 BDA, 15 MR) 126 (111 BSI, 15 MR)
Parameters sampled Organic matter yes yes yes
Photosynthetic pigments no yes yes
Sediment grain-size yes yes yes
Heavy-metals yes yes (for a limited number of stations) no (interpolated based on 2014 and 2016 values)
Benthic communities Compartment targeted Macro-infauna Macro-infauna Macro-infauna
Sieved used 500 µm 1 mm 500 µm and 1 mm
Conservation technique Formaldehyle Formaldehyle Formaldehyle
Others N.A. N.A. N.A.

We used data from subtidal ecosystems (see metadata files for more information). Only stations that have been sampled both for abiotic parameters and benthic species were included.

Selected variables for the analyses:

Abundances of Bipalponephtys neotena (Bneo) and Spisula solidissima (Ssol) were also considered (see IndVal and SIMPER results).

Statistics for each variable considered:

  Min Max Median Mean SD SE 95% CI
depth 4.000 9.600 7.250 6.970 1.611 0.255 0.499
om 0.187 8.260 0.868 1.368 1.465 0.232 0.454
gravel 0.000 0.481 0.000 0.017 0.076 0.012 0.024
sand 0.000 1.000 0.000 0.148 0.358 0.057 0.111
silt 0.000 0.022 0.001 0.004 0.006 0.001 0.002
clay 0.000 1.000 0.992 0.830 0.361 0.057 0.112
arsenic 1.100 6.000 2.250 2.720 1.259 0.199 0.390
cadmium 0.030 0.220 0.110 0.116 0.045 0.007 0.014
chromium 10.900 143.300 63.200 65.520 29.623 4.684 9.180
copper 2.200 32.400 7.300 11.045 8.675 1.372 2.688
iron 14089.920 188857.220 60284.230 64222.926 31677.444 5008.644 9816.761
manganese 251.670 5962.190 1106.625 1412.044 1050.987 166.176 325.698
mercury 0.000 0.250 0.000 0.014 0.043 0.007 0.013
lead 1.020 12.180 3.110 4.308 2.945 0.466 0.913
zinc 15.900 101.500 45.150 53.163 23.870 3.774 7.397
S 5.000 28.000 14.000 16.275 7.035 1.112 2.180
N 12.000 2100.000 173.500 634.000 702.288 111.041 217.637
H 0.776 2.364 1.800 1.694 0.386 0.061 0.120
J 0.294 0.935 0.636 0.640 0.152 0.024 0.047

1. Maps

1.1. General map

1.2. Parameters maps

For maps of heavy metal concentrations, stations have been grouped based on Environment Canada (2007) classification of sediment toxicity (grey = low toxicity, red = high toxicity).

OM

Gravel

Sand

Silt

Clay

Arsenic

Cadmium

Chromium

Copper

Iron

Manganese

Mercury

Lead

Zinc

Bneo

Pste

Ssol

Epar

Species richness

Total abundance

Shannon index

Piélou’s evenness

2. Figures

2.1. Barplots

Organic matter

Grain-size

Heavy metals

Species abundances

Diversity indices

2.2. Phylum frequencies

Phylum abundances by condition
Phylum HI R
Annelida 20340 1042
Phoronida 1138 2
Arthropoda 871 746
Mollusca 341 725
Platyhelminthes 5 0
Echinodermata 4 139
Hemichordata 2 0
Brachiopoda 0 0
Cnidaria 0 0
Nematoda 0 0
Nemertea 0 5

2.3. Species estimation curves

2.4. Principal Component Analysis

Parameters + Metals

Variables have been scaled by mean and standard-deviation prior to analysis.

Parameters

Variables have been scaled by mean and standard-deviation prior to analysis.

Metals

Variables have been scaled by mean and standard-deviation prior to analysis.

2.5. Non-metric Multidimensional Scaling

Parameters + Metals

Variables have been scaled by mean and standard-deviation prior to analysis.

Parameters

Variables have been scaled by mean and standard-deviation prior to analysis.

Metals

Variables have been scaled by mean and standard-deviation prior to analysis.

Species

Stations with no species are deleted from this analysis.

2.6. Hierarchical Agglomerative Clustering

Parameters + Metals

Variables have been scaled by mean and standard-deviation prior to analysis.

##  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 
##  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  2  1  1  3  1  3  3  3  3  3  2  3  3  3  2  2  3  2  3  2  3  3  3 
## 39 40 
##  3  3

Parameters

Variables have been scaled by mean and standard-deviation prior to analysis.

##  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 
##  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  2  1  1  1  1  3  3  3  3  3  2  3  3  3  2  2  3  2  3  2  3  3  3 
## 39 40 
##  3  3

Metals

Variables have been scaled by mean and standard-deviation prior to analysis.

##  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 
##  1  2  1  1  1  1  2  1  1  1  2  3  2  2  2  3  3  2  2  2  2  2  2  3  2  3  3  3  3  3  3  3  3  3  3  2  2  3 
## 39 40 
##  3  3

Species

Stations with no species are deleted from this analysis.

##  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 
##  1  1  1  1  1  1  1  1  1  1  1  1  1  1  1  2  2  2  2  1  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2  2 
## 39 40 
##  2  2

Elliot Dreujou

2019-12-14